TABLE 2.
Cryo-EM data collection, refinement, and validation statistics
| Parameter | P9-1 decamer (D5) | P9-1 dodecamer (D6) |
|---|---|---|
| Data collection and processing | ||
| Microscope | Talos Arctica | Talos Arctica |
| Voltage (kV) | 200 | 200 |
| Detector | FEI Falcon III | FEI Falcon III |
| Magnification | 120,000 | 120,000 |
| Electron exposure (e–/Å2) | 30 | 30 |
| Defocus range (μm) | −0.8 to −3.8 | −0.8 to −3.8 |
| Pixel size (Å) | 0.855 | 0.855 |
| Symmetry imposed | D5 | D6 |
| Initial particle images (no.) | 202,824 | 202,824 |
| Final particle images (no.) | 99,682 | 22,510 |
| Map resolution (Å) | 4.7 | 6.8 |
| FSC threshold | 0.143 | 0.143 |
| EMDB code | EMD-23046 | EMD-23047 |
| Model refinement | ||
| Initial model used (PDB code) | 6UCT | 6UCT |
| Unmasked resolution at 0.5/0.143 FSC (Å) | 5.3/4.7 | 7.1/5.6 |
| Masked resolution at 0.5/0.143 FSC (Å) | 5.2/4.6 | 7.0/5.6 |
| No. of protein atoms | 21,920 | 26,304 |
| No. of ligand atoms | - | - |
| No. of water molecules | - | - |
| B factors (Å2) | 170 | 175 |
| RMSD from ideal values (87) | ||
| Bond lengths (Å) | 0.005 | 0.004 |
| Bond angles (°) | 0.846 | 1.008 |
| Validation (32) | ||
| MolProbity score (percentile) | 2.57 (43rda) | 2.52 (46tha) |
| CC (mask) | 0.82 | 0.75 |
| Ramachandran plot | ||
| Favored (%) | 89.3 | 91.2 |
| Allowed (%) | 10.7 | 8.8 |
| Disallowed (%) | 0 | 0 |
| Cβ outliers (%) | 0 | 0 |
| CaBLAM outliers (%) | 1.7 | 2.5 |
| Cα geometry outliers (%) | 0.4 | 0.4 |
| PDB code | 7KVC | 7KVD |
a
The 100th percentile indicates the best structures of comparable resolution; the 0th percentile indicates the worst structures.